I still get permission denied sometimes. I still do not always know if I need sudo or not for a command. But it I get permission denied I try again with sudo.
If BIOS is not seeing hard drives nothing will boot. Double check that connections, both power & signal are correct.
After you install Ubuntu then it would update to add other systems with the sudo update-grub if not already in grub menu.
You have to run chkdsk from a Windows XP install disk or a newer Windows repairCD or flash drive. I have used a Windows 7 repair flash drive to run chkdsk on my now not used XP install. It worked better or fixed some things (or so it said) that the XP chkdsk did not. But it converted PBR or partition boot sector to Windows 7 type and I had to do another repair to fix that.